Hi all! Currently I have the same bug, though my game is not that heavily modded! For me it started happening after I picked up Serana (Dawnguard DLC) an travelled with her to Whiterun. The first hostile NPC was Uthgerd the Unbroken, I pacified her by using "SetAV Aggression to 0", Next was Elrindir at The Drunken Huntsman, first he fled, and later he started attacking. The moment I gave up with the "SetAV Aggression to 0" was when I entered Dragonreach, and everyone was aggressive, even the children! This is my current Load Order: I'll try the fix with the Bounty, but instead of attacking a guard you could also use the Console Commands:
player.paycrimegold <X> <Y> <FactionID>
On occasion, this may not pay off the entire bounty
X = 1 Remove stolen items. 0 Do not remove stolen items.
Y = 1 Go to jail. 0 Do not go to jail.
Or else
player.setcrimegold <#> <FactionID>
For all the Faction ID's (on top) https://elderscrolls.fandom.com/wiki/Console_Commands_(Skyrim)/Factions *EDIT* That seems to have worked! Thank you so much for the suggestion. My steps: 1. Open Console (~ key) 2. Type "Player.GetCrimeGold 267ea" (To check current Crime Gold in Whiterun, it read 0, as expected.) 3. Type "Player.SetCrimeGold 1 267ea" (To set the CrimeGold to 1 Gold in Whiterun.) 4. Type "Player.PayCrimeGold 0 0 267ea" (To Pay the CrimeGold, without Items being Confiscated nor needing to go to Jail, in Whiterun.) All aforementioned NPC where no longer hostile!